Up: Component summary Component

AligFilterFlag

Allows to filter SAM files with alignments using the flag field. The alignment file is split in two based on the value given in the flag parameter. For example if flag=64, the files are split based on if the reads are the first or the second mate of the pair end read. A list of flags can be used as well. Other possible values for flag are:

*The value used for flag is the one specified in parenthesis in this list. Example: flag=1,8,16

Version 1.1
Bundle sequencing
Categories
Authors Alejandra Cervera (alejandra.cerverataboada@helsinki.fi)
Issue tracker View/Report issues
Requires python
Source files component.xml flag.py
Usage Example with default values

Inputs

Name Type Mandatory Description
alignment SAM Mandatory A SAM file with the alignments.

Outputs

Name Type Description
splitAlignments1 SAM Alignments with the flag value.
splitAlignments2 SAM Rest of the alignments.

Parameters

Name Type Default Description
flag string "64" The flag value to use for filtering, default is 64 which separates alignments based on first or second pair from a paired end read

Test cases

Test case Parameters IN
alignment
OUT
splitAlignments1
OUT
splitAlignments2
case1 properties alignment (missing) (missing)

# Testing AligFilterFlag component,
flag = 1,8,16


Generated 2018-12-12 07:42:05 by Anduril 2.0.0